Protein Counterpoint Sonification

We are researching the use of algorithmic composition to generate counterpoint through fracture. Driven by the universal physical forces near a singularity, captured in the so-called Cauchy stress tensor (read more about it here: en.wikipedia.org/wiki/Cauchy_stress_tensor), we are creating patterns of interdependent polyphony through independent patterning in time and pitch.

FRACTURES ARE UNIVERSAL

A fracture is a crack in a material (often seen in glass, but also represented in earthquakes when tectonic plates fracture, or in the unfolding of a protein). Fracturing is the process of destruction of structure, and hence is the division between function and failure in material and has correspondences in philosophy. The tipping point of the crack, the locality of greatest action, and where bond breaking occurs, is the singular crack tip, the sharp edge.
All fractures feature a universal distribution of stresses – the forces that act inside the material and which stretch/compress chemical bonds. No matter what material, as you get closer to the singularity – the tip of the crack – the distribution of forces are identical.

In the three pieces in this set, we explore these universal features to generate algorithmically composed music. We try to explore whether the universal features of fractures have the capacity to generate counterpoint – universal features of music, to better understand the analogy across manifestations.
Read more about the physics of fracture in [1].


Fracture-generated counterpoint hence may reflect the universal features of fractures and provides a model thereof. Owing to the universal significance of fracturing as a process in material and amaterial manifestations, the musical effects generated hereby can be an interesting subject of further analysis and inspiration.

[1] M. Buehler, Atomistic Modeling of Materials Failure, 2008 www.springer.com/gp/book/9780387764252

Counterpoint Through Fracture

Inspiration from Nature knows no boundary and can take on unusual forms.

Fire has fascinated humankind since the prehistoric era. Rooted in the interactions between sound and flames, we report a method to use fire for a variety of purposes, including sonification, art, and the design and manufacturing nature-inspired materials.

We present a method to sonify fire, thereby offering a translation from the silent nature of flames, to represent audible information, and to generate de novo flame images.

To realize material specimen derived from fire, we use the autoencoder to generate image stacks to yield continuous three dimensional geometries that are manufactured using 3D printing.

This represents the first generation of nature-inspired audible signals from fire, and can be a platform to be used for other natural phenomena in the quest for de novo architectures, geometries, and design ideas, thus creating additional directions in artistic and scientific research through the creative manipulation of data with structural similarities across fields.

Original paper: https://www.cell.com/iscience/fulltext/S2589-0042(21)00841-5

Fire sonification: Making silent flames audible

Deep Aria: The First Conversation is an operatic meditation on the very first act of communication in the universe - long before voices, before language, before sound itself. This piece traces the ancient dialogue encoded in the folding of matter: proteins bending into meaning, forces negotiating with chance, structure learning how to speak through form.

The vocals emerge like a memory from deep time: a single motif rising out of silence, evolving into a resonance that travels from molecule to cell, from organism to mind. Each phrase is a variation on the primordial exchange that shaped life’s architecture.

This is an aria of origin - where creativity echoes the first fold, and human imagination becomes the latest instrument in a conversation billions of years old.

This is a reflection on the earliest correspondence, where tension became shape, shape became message, an exchange between what could exist and what had not yet chosen to.

Lyrics

Before life, before silence could be named,
a faint inflection of matter
bent inward—
a pre-formal whisper,
a fold rehearsing its first message.

Deep time thickened around this gesture.
Not sound, not syntax,
only a correspondence of forces,
an exchange between what could exist
and what had not yet chosen to.
The first communication
was a tension becoming shape.

Proteins emerged as answers
to questions no voice had asked—
each helix a reply to gravity,
each sheet a response to water’s touch.
Creation was not an event
but a conversation,
where structure negotiated with chance
and time learned to listen.

Across epochs, the aria propagated:
molecule speaking to molecule,
cell murmuring to cell,
organism unfolding toward organism—
a communication so ancient
that even light could not recall its origin.
Life became a network of resonances,
its messages encoded in angles and bonds,
its meaning carried in the way form
leaned toward possibility.

Human creativity rose much later,
an aftershock of those early dialogues.
Our art, our mathematics,
our impulse to build symmetries in sound—
all are descendants of that primordial exchange.
When we compose, design, imagine,
we reenact the first folding,
carrying forward the deep-time message
that difference can be organized,
that variation can speak.

Goldberg Inceptionism mirrors this ancestry:
variations dreaming themselves,
structures communicating across scales,
a recursion of understanding
that remembers what matter once felt
when it first tried to become alive.

In this unending Aria,
communication is creation—
a message passed
from protein to organism,
from organism to mind,
from mind back to matter.
We are its latest motif,
still learning how to hear
the conversation that began
the world of life.

Deep Aria: The First Conversation

Topology Koto is a molecular aria where protein folding becomes music. A koto traces the amino-acid backbone of 1AKG—venom from the cone-shell snail—while strings, winds, and brass translate sequence into structure, tension into harmony. This piece reveals the hidden topology of matter as sound: the whisper of a toxin, the rise of helices, and the quiet symmetry of immune defense, together unfolding in a single resonant chain.


Koto of Topology

This track tells the story of a molecule learning to move, groove, and become itself. In the quiet beneath the atoms — where rhythm starts before sound exists — a single protein chain awakens. Its sequence of twenty letters is a coded spell, a secret funk riff trying to find the right shape to lock into the groove. The track follows its journey as it folds, twists, and snaps into form, each structural change expressed not through classical majesty but through funky micro-gestures: bass pops as torsion, koto plucks as backbone shifts, brass bursts as buried emotional residues rising to the surface.

-As the chain folds, each instrument maps to a part of its structure.
-Koto scratches outline the backbone like a funk rhythm guitar.
-Cello and double bass pump out the deep, oceanic pocket—the primordial groove.
-Flute and flugelhorn paint shimmering edges, glinting like solvent-exposed surfaces.
-Viola, violins glide like sliding chromatic fills, revealing hidden pockets and motifs.

The protein comes alive through call-and-response, through rhythmic signatures that echo beta-sheets, helical rises, and tertiary blossoms. Every attack, rest, and harmonic tension mirrors the physical dance of folding.

Topology

Composed originally as part of a series for chamber orchestra, this piece traces slow-evolving ‘protein resonances’ across piano and solo strings. The themes move with the gentle, drifting motion of a jellyfish - long arcs, suspended tones, and gradual harmonic bloom. Here, this work is re-imagined through a rock lens, performing it on electric guitar with expressive, high-gain phrasing. The result is a distilled soliloquy: orchestral DNA transformed into a raw, lyrical electric voice.

Soliloquy of Fire

The album artwork depicts a grand piano trapped within a fracturing snow globe, bathed in warm, nostalgic sepia tones. The crack in the glass and the snow spilling onto the table suggest the fragility of memory and the failure of trying to perfectly preserve the past. It creates a poignant tension between the silence of the enclosed instrument and the breaking of its protective world. 


Broken Beat (Piano)

Broken, meditative beat, performance in an ambient void. The visual shows how the music is carving out the space - the ice tunnel is essentially a visualization of the sound waves pushing through a solid medium, breaking and assembling, creating form. The "broken" nature of the beat mirrors the cracks in the ice floor. The beauty of the music is disrupting the frozen, static environment. 

Broken Beat (Ambient)

A Garden of Flowers (Solo Piano) revisits a series of works originally composed thirty years ago as electronic music. These pieces have been rewritten and reimagined for solo piano, preserving their underlying structures and motifs while translating them into an acoustic, tactile, and emotive form. The album explores how ideas persist across time and medium, allowing patterns once conceived through electronic synthesis to emerge through touch, resonance, and silence into organic form.

The Truth Is A Virus (Solo Piano)

Geltung (Solo Piano)

The Sun and Freedom (Solo Piano)

A Garden of Flowers revisits a series of works originally composed as electronic music. For this release, the pieces have been reinterpreted and recomposed in an ambient form, preserving their underlying structures and motifs while reshaping them through texture, space, and gradual transformation.  The album treats recomposition as a form of reflection, allowing ideas to unfold more slowly and to breathe.

Accident (Ambient Acid)

Danger (Ambient)

Idea (Ambient)

Strings in Dublin (Ambient)

The Truth Is a Virus (Ambient Trance)

Strings in Dublin (Ambient Instrumental)

The Truth Is a Virus (Ambient)

Geltung (Ambient)

The Sun and Freedom (Ambient)

Close to Nature (Ambient)

Ballad (Ambient)

Recently (Ambient Acid)

A Garden of Flowers (Ambient)

Crying Beat is a rewrite of original material from The Green Album. The piece is rebuilt around breakbeats, a 909 foundation, extremely low-tuned, traveling hi-hats, and a 303 line that shifts between propulsion and distortion. In returning to this track, I was interested in what happens when an early idea is pushed through a more deliberate rhythmic and texturally complex language. I focused on groove, timbre, and motion as the primary carriers of expression. The piece is shaped by distance, experience, and a deeper attention to rhythm.

Crying Beat (303 Ambience)

Crying Beat (Acid Break)

We introduce materiomusic as a generative framework linking the hierarchical structures of matter with the compositional logic of music. Across proteins, spider webs, and flame dynamics, vibrational and architectural principles recur as tonal hierarchies, harmonic progressions, and long-range musical form. Using reversible mappings, from molecular spectra to musical tones and from three-dimensional networks to playable instruments, we show how sound functions as a scientific probe, an epistemic inversion where listening becomes a mode of seeing and musical composition becomes a blueprint for matter. These mappings excavate deep time: patterns originating in femtosecond molecular vibrations or billion-year evolutionary histories become audible. We posit that novelty in science and art emerges when constraints cannot be satisfied within existing degrees of freedom, forcing expansion of the space of viable configurations. Selective imperfection provides the mechanism restoring balance between coherence and adaptability. Quantitative support comes from exhaustive enumeration of all 2^12 musical scales, revealing that culturally significant systems cluster in a mid-entropy, mid-defect corridor, directly paralleling the Hall-Petch optimum where intermediate defect densities maximize material strength. Iterating these mappings creates productive collisions between human creativity and physics, generating new information as musical structures encounter evolutionary constraints. We show how swarm-based AI models compose music exhibiting human-like structural signatures such as small-world connectivity, modular integration, long-range coherence, suggesting a route beyond interpolation toward invention. We show that science and art are generative acts of world-building under constraint, with vibration as a shared grammar organizing structure across scales. The framework supports multimodal de novo protein design and AI systems that invent through collective dynamics.

Podcast: Selective Imperfection as a Generative Framework for Analysis, Creativity and Discovery

Green Ambience is a re-release of the "Green Album" - revisited with a focus on space, tone, and long-form development. I composed the originals in the 1990s, and this release preserves their core motifs while presenting them through a quieter, more ambient lens: slow-evolving textures, organic rhythmic motion, and occasional acid-house circuitry that surfaces and recedes like a pulse in the dark.

The tracklist is sequenced as the main album first, followed by a Versions section. The primary run is the intended narrative arc; the alternate mixes are included as companion perspectives (different edits, energies, and room acoustics around the same underlying material). They document how the same themes can be heard at different scales: immersive and spacious in the long forms, sharper and more kinetic in the edits.

Feel So Good

Crying Beat (Extended Mix)

Echo Garden

Blocking

Nobody Else

Citrus Circuit

Mystic

Rocking Chair

Nobody Else (Trance Mix)

Citrus Circuit (Extended Mix)

Flight to Nowhere

Thoughts on a Green Day

Going deeper inside a spider web. Multiple spider web variations interact across a spectrum of sonic textures. The sounds are based on a sonification method of a spider web as described in the references below [1-2], part of a larger collaboration with Tomás Saraceno, Saraceno Studios, Ally Bisshop, Thomas Muehletahler, and Evan Ziporyn, and the MIT Center for Art, Science and Technology (CAST).

Several individual webs constructed by Cyrtophora citricola are played in this piece, creating an overlaying soundscape of different shades. The piece includes a rhythm track for added structure, but all other sounds you hear are generated from the sonification of the spider web. 

The image [3] shows a 3D spider web, lit up using a green laser during scanning. The spider is visible in the top middle as she constructs the web. 

References:

[1] Su, I.; Qin, Z.; Saraceno, T.; Krell, A.; Mühlethaler, R.; Bisshop, A.; Buehler, M. J. Imaging and Analysis of a Three-Dimensional Spider Web Architecture. J. R. Soc. Interface 2018, 15 (146), 20180193. doi.org/10.1098/rsif.2018.0193.

[2] Su, I.; Qin, Z.; Bisshop, A.; Muehlethaler, R.; Ziporyn, E.; Buehler, M. J. Sonification of a 3D Spider Web and Reconstitution into Musical Composition Using Granular Synthesis. in submission

[3] Image by I. Su, MIT and M. Buehler, of a tidarren sisyphoides spider building a web, in collaboration with Tomas Saraceno Studio (Berlin)

Spider Variations

What you hear is the sonified expression of the 3D structure of the protein with PDB ID 1akg (ALPHA-CONOTOXIN PNIB FROM CONUS PENNACEUS, see: http://dx.doi.org/10.2210/pdb1AKG/pdb), translated into an orchestral setting (koto [a Japanese string instrument], cello, double bass, viola, flute, and fluegelhorn). The koto is used to express the primary, secondary and tertiary structure of the protein.  

The piece reflects a classical period model of the hierarchical mapping to describe the 3D folded structure of a protein in musical space. The musical mapping begins from the primary amino acid sequence (GCCSLPPCALSNPDYCX) and encodes multiple hierarchical structural levels, and adds musical experimentation. 

We use the concept proposed by Yu, Buehler et al. (ACS Nano) to map amino acid sequences to music, and augment the mapping by adding more data. The 3D folded structure of a protein is coded by inserting strummed chords and interwoven melodies that code for the geometric arrangement of amino acids, the protein's tertiary structure. Rhythm and note volume code for secondary structure.

[1] The protein used for this example is 6cjc (CRYSTAL STRUCTURE OF A FC FRAGMENT LALA MUTANT (L234A, L235A) OF HUMAN IGG1 (CRYSTAL FORM 3))

[2] https://doi.org/10.1021/acsnano.9b02180

Koto Ensemble of Protein 1akg (Venom of Predatory Marine Snails)

Sounds of the escherichia virus T4,  a species of bacteriophages that infect Escherichia coli bacteria. What you hear is the sonified expression of the 3D structure of the protein needle at the core of this virus, classified in the protein data bank with ID 4osd (triple-stranded beta-helix comprising the central spike of bacteriophage T4. 

See http://dx.doi.org/10.2210/pdb4OSD/pdb for more information.  

The music represents the spike-shaped protein that functions to disrupt the membrane of the target cell during phage infection. The protein structure has first been reported in [1].

The protein structure is translated into an orchestral setting (koto [a Japanese string instrument], cello, double bass, viola, flute, and a range of other orchestral instruments). The various instruments is used to express the primary, secondary and tertiary structure of the protein. The piece is composed of a A-B-A' structure, where A and A' reflect the beginning and end coding of the protein, the B part represents the coding of the primary backbone sequence and structure. 

The track image shows a picture of this protein, reflecting a highly organized, repetitive structure with continuous slight variations, which is also reflected musically. The extensive length of 40+ minutes is due to the long protein chains included in this protein assembly. 

The piece reflects a classical period model of the hierarchical mapping to describe the 3D folded structure of a protein assembly (consisting of 9 protein chains) in musical space. The musical mapping begins from the primary amino acid sequence and encodes multiple hierarchical structural levels, and is complemented with musical experimentation. 

We use the concept proposed by Yu, Buehler et al. (ACS Nano) [2] to map amino acid sequences to music, and augment the mapping by adding more data. The 3D folded structure of a protein is coded by inserting strummed chords and interwoven, cascaded melodies and rhythms that code for the geometric arrangement of amino acids, the protein's tertiary structure. Rhythm and note volume code for secondary structure.

References:

[1] Original research paper describing the gp5β-BC2 fragment: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576200/

[2] https://doi.org/10.1021/acsnano.9b02180

[3] Track image shows the phage, a virus that infects and replicates within bacteria and archaea (source: Wikipedia, by: Adenosine, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=8643737, depicting the structure of a typical myovirus bacteriophage)

Viral koto ensemble of protein 4osd with cello, violin, flute and bass

In this piece we use algorithmic composition to generate counterpoint  through fracture. We are creating interdependent polyphony through independent patterning in time and pitch, driven by the universal physical forces near a singularity. 

FRACTURES ARE UNIVERSAL 

A fracture is a crack in a material (often seen in glass, but also represented in earthquakes when tectonic plates fracture, or in the unfolding of a protein). Fracturing is the process of destruction of structure, and hence is the division between function and failure in material and has correspondences in philosophy. The tipping point of the crack, the locality of greatest action, and where bond breaking occurs, is the singular crack tip, the sharp edge. 

All fractures feature a universal distribution of stresses – the forces that act inside the material and which stretch/compress chemical bonds.  No matter what material, as you get closer to the singularity – the tip of the crack – the distribution of forces are identical. 

Here we explore these universal features to generate algorithmically composed music. We try to explore whether the universal features of fractures have the capacity to generate counterpoint – universal features of music, to better understand the analogy across manifestations. 

Read more about the physics of fracture in [1].

HOW THE MUSIC IS CREATED

A set of Euclidean rhythmic motifs (with sparsity: 1/3, 5/12, and 7/12 to reflect different atomic organizations in crystalline forms) are acted upon based on the principal stresses near a crack under tensile loading.  We use the singular principal stress field to drive melodic content formation, whereas several independent moving observers assess the local principal stresses. The observes move in circular fashion, towards and away from the singularity in a spiral, oscillatory motion (see track image).  

Each individual note played is generated based on physical model of a string exposed to different stress levels. Hence, large stresses pull notes into high pitch, lower stresses compress it to lower pitches. 

The violent nature of forces experienced by the observer circling around the crack tip generate complex but highly organized melodic forms. As the stress field features universal, respective patterning, the various melodic lines generated have relationships rooted in the nanoscale physics surrounding the singularity. 

Fracture-generated counterpoint hence may reflect the universal features of fractures and provides a model thereof. Owing to the universal significance of fracturing as a process in material and amaterial manifestations, the musical effects generated hereby can be an interesting subject of further analysis and inspiration. 

[1] M. Buehler, Atomistic Modeling of Materials Failure, 2008 https://www.springer.com/gp/book/9780387764252

Counterpoint Through Fracture: Part I – Spiral Movers

For piano. We are researching the use of algorithmic composition to generate counterpoint through fracture. Driven by the universal physical forces near a singularity, captured in the so-called Cauchy stress tensor (read more about it here: https://en.wikipedia.org/wiki/Cauchy_stress_tensor), we are creating interdependent polyphony through independent patterning in time and pitch. 

FRACTURES ARE UNIVERSAL

A fracture is a crack in a material (often seen in glass, but also represented in earthquakes when tectonic plates fracture, or in the unfolding of a protein). Fracturing is the process of destruction of structure, and hence is the division between function and failure in material and has correspondences in philosophy. The tipping point of the crack, the locality of greatest action, and where bond breaking occurs, is the singular crack tip, the sharp edge.

All fractures feature a universal distribution of stresses – the forces that act inside the material and which stretch/compress chemical bonds. No matter what material, as you get closer to the singularity – the tip of the crack – the distribution of forces are identical.

In this study we explore these universal features to generate algorithmically composed music. We try to explore whether the universal features of fractures have the capacity to generate counterpoint – universal features of music, to better understand the analogy across manifestations.

Read more about the physics of fracture in [1].

HOW THE MUSIC IS CREATED

The piece is constructed from multiple movers in the singular stress field, and using the full stress tensor to derive musical structure. The observes move in circular fashion around the singularity in an oscillatory motion.  Each individual note played is generated based on the stress tensor, a physical quantity that describes the forces inside a material. Large stresses pull notes into high pitch, lower stresses compress it to lower pitches.

The violent nature of forces experienced by the observer circling around the crack tip generate complex but highly organized melodic forms. As the stress field features universal, respective patterning, the various melodic lines generated have relationships rooted in the nanoscale physics surrounding the singularity.

Fracture-generated counterpoint hence may reflect the universal features of fractures and provides a model thereof. Owing to the universal significance of fracturing as a process in material and amaterial manifestations, the musical effects generated hereby can be an interesting subject of further analysis and inspiration.

[1] M. Buehler, Atomistic Modeling of Materials Failure, 2008 www.springer.com/gp/book/9780387764252

Counterpoint Through Fracture: Part II - Stress Tensor Variations

This piece is a reprise of the motifs presented in Part I, now set into a more complex musical arrangement, and with more rhythmic guidance. 

As the other compositions in this series, this part is created based on the universal stress field of a crack, exploiting the unique features of the singular stress tensor to derive melodic and counterpunctual content through overlapping stress fields. 

GENERAL FEATURES: FRACTURES ARE UNIVERSAL 

A fracture is a crack in a material (often seen in glass, but also represented in earthquakes when tectonic plates fracture, or in the unfolding of a protein). Fracturing is the process of destruction of structure, and hence is the division between function and failure in material and has correspondences in philosophy. The tipping point of the crack, the locality of greatest action, and where bond breaking occurs, is the singular crack tip, the sharp edge. 

All fractures feature a universal distribution of stresses – the forces that act inside the material and which stretch/compress chemical bonds.  No matter what material, as you get closer to the singularity – the tip of the crack – the distribution of forces are identical. 

Here we explore these universal features to generate algorithmically composed music. We try to explore whether the universal features of fractures have the capacity to generate counterpoint – universal features of music, to better understand the analogy across manifestations. 

Read more about the physics of fracture in [1].

HOW THE MUSIC IS CREATED

A set of Euclidean rhythmic motifs (with sparsity: 1/3, 5/12, and 7/12 to reflect different atomic organizations in crystalline forms) are acted upon based on the principal stresses near a crack under tensile loading.  We use the singular principal stress field to drive melodic content formation, whereas several independent moving observers assess the local principal stresses. The observes move in circular fashion, towards and away from the singularity in a spiral, oscillatory motion (see track image).  Large stresses pull notes into high pitch, lower stresses compress it to lower pitches.  These motions provide the basis for the music you hear. 

The violent nature of forces experienced by the observer circling around the crack tip generate complex but highly organized melodic forms. As the stress field features universal, respective patterning, the various melodic lines generated have relationships rooted in the nanoscale physics surrounding the singularity. 

Fracture-generated counterpoint serves as a means to explore the universal features of fractures, and provides a model thereof. Owing to the universal significance of fracturing as a process in material and amaterial manifestations, the musical effects generated hereby can be an interesting subject of further analysis and inspiration. 

[1] M. Buehler, Atomistic Modeling of Materials Failure, 2008 https://www.springer.com/gp/book/9780387764252

Counterpoint Through Fracture: Part III - Spiral Roosters

This piece is an illustration how fractures can be used to design sound, here realized in a fracture drone. The piece is constructed from a single sine wave, by using several independent movers in the singular fracture stress field (see more details on the method in the description of Parts I and II). 

All 9 movers live within the fracture stress field and move stochastically (in angle, distance to singularity, stress intensity factor).  Additional harmonic content is derived from the melodies constructed in Part II. 

FRACTURES ARE UNIVERSAL

A fracture is a crack in a material (often seen in glass, but also represented in earthquakes when tectonic plates fracture, or in the unfolding of a protein). Fracturing is the process of destruction of structure, and hence is the division between function and failure in material and has correspondences in philosophy. The tipping point of the crack, the locality of greatest action, and where bond breaking occurs, is the singular crack tip, the sharp edge.

All fractures feature a universal distribution of stresses – the forces that act inside the material and which stretch/compress chemical bonds. No matter what material, as you get closer to the singularity – the tip of the crack – the distribution of forces are identical.

In this composition we explore these universal features to generate algorithmically composed music. We try to explore whether the universal features of fractures have the capacity to generate counterpoint – universal features of music, to better understand the analogy across manifestations.

Read more about the physics of fracture in [1].

[1] M. Buehler, Atomistic Modeling of Materials Failure, 2008 www.springer.com/gp/book/9780387764252

Counterpoint Through Fracture: Part IV - Fracture Drone

This piece is a sonification of the spike protein of the pathogen of COVID-19, 2019-nCoV (protein data bank identifier 6VSB [1]). What you hear is a multi-layered sonification approach featuring both the vibrational spectrum of the entire protein (expressed in sound and rhythmic elements), as well as the sequence and folding of amino acids that compose the virus spike structure [2]. 

References
[1] Wrapp et al., "Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation," Science, 2020, DOI: 10.1126/science.abb2507
[2] Buehler et al., "A Self-Consistent Sonification Method to Translate Amino Acid Sequences into Musical Compositions and Application in Protein Design Using Artificial Intelligence," ACS Nano, 2019, DOI: https://pubs.acs.org/doi/10.1021/acsnano.9b02180

Sonification of a virus spike protein

Sonification of the Coronavirus Spike Protein (Amino Acid Scale)

While we cannot see small nanoscopic objects like proteins or other molecules that make up virtually all living matter including our cells, tissues, as well as pathogens such as viruses, our computational algorithm allows us to make its material manifestation audible.  This piece is a musical representation of the amino acid sequence and structure of the spike protein of the pathogen of COVID-19, 2019-nCoV (protein data bank identifier 6VSB [1]). 

MUSICAL DECEIT

A virus’ genome hijacks the host cell’s protein manufacturing machinery, and forces it to replicate the viral genome and produce viral proteins to make new viruses from it.  This musical art teaches us something about the fine line between beauty of life and death as an opposite pole.  As you listen to the protein you will find that the intricate design results in incredibly interesting and actually pleasing, relaxing sounds. This doesn’t really convey the deadly impacts this particularly protein is having on the world. This aspect of the music shows the deceiving nature of the virus, how it hijacks our body to replicate, and hurt us along the way. So, the music is a metaphor for this nature of the virus to deceive the host and exploit it for its own multiplication. 

HOW IT IS DONE: 

What you hear is a multi-layered algorithmic composition featuring both the vibrational spectrum of the entire protein (expressed in sound and rhythmic elements), the sequence and folding of amino acids that compose the virus spike structure, as well as interwoven melodies - forming counterpoint music - reflecting the complex hierarchical intersecting geometry of the protein [2].

Scientific references:

[1] Wrapp et al., "Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation," Science, 2020, DOI: 10.1126/science.abb2507

[2] Buehler et al., "A Self-Consistent Sonification Method to Translate Amino Acid Sequences into Musical Compositions and Application in Protein Design Using Artificial Intelligence," ACS Nano, 2019, DOI: pubs.acs.org/doi/10.1021/acsnano.9b02180

Viral counterpoint of the coronavirus spike protein (2019-nCoV)

Viral Counterpoint of the Coronavirus Spike Protein (2019-nCoV)

This is a sonification of a protein extracted from honeybees, and folded using a deep learning method described in [1].

BACKGROUND:

The development of rational techniques to discover new mechanically relevant proteins for use in variety of applications ranging from mechanics, agriculture to biotechnology remains an outstanding nanomechanical design problem. The key barrier is to design a sequence to fold into a predictable structure to achieve a certain material function. Focused on alpha-helical proteins (as found in skin, hair, and many other mechanically relevant protein materials), we report a Multi-scale Neighborhood-based Neural Network (MNNN) model to learn how a specific amino acid sequence folds into a protein structure. 

The algorithm predicts the protein structure without using a template or co-evolutional information at a maximum error of 2.1 Å. We find that the prediction accuracy is higher than other models and the prediction consumes less than six orders of magnitude time than ab initio folding methods. We demonstrate that MNNN can predict the structure of an unknown protein that agrees with experiments, and our model hence shows a great advantage in the rational design of de novo proteins.

Reference: Z. Qin, B. Marelli, M.J. Buehler, et al., "Artificial intelligence method to design and fold alpha-helical structural proteins from the primary amino acid sequence," Extreme Mechanics Letters, Vol. 36, p. 100652, 2020 https://doi.org/10.1016/j.eml.2020.100652

Honeybee Silk

This piece explores melodic and rhythmic content from a variety of protein structures, including the binding event of COVID-19 to human cells. The progression models pre-pandemic humanity and the virus alone ("growth"), then the virus interacting with human cell - a struggle modeling repeated infection of new cells ("infection") - and finally back to virus alone overlaid with the regular rhythm of human life ("release").  As expressed musically, life after the virus is different than before , since we all changed due to the pandemic. How, we do not know yet. 

LYRICS:

Growth, Infection and Release.
Growth represents prepandemic humanity and the virus alone.
Infection represents the period during with the virus is interacting with human cells.
There is a struggle between infection of new cells and human defenses.
Finally, we return to the regular rhythm of human life, the release.
Life after the virus is different than before. We all changed due to the pandemic.
How we have changed, we do not know yet.

MORE DETAILS:

The rhythm is derived directly from the vibrational spectrum of the virus spike protein attached to the human ACE2 receptor, scaled to the frequencies that human ears perceive as rhythm. 

The construction of this piece involves the vibrational frequencies of virus proteins alone, melding into overlays of the virus with human proteins attached, peaking and then decaying as the virus releases its grip on humanity.  The piece ends with the steady motions of human existence, as we enter release.

The entire composition is written in the amino acid scale, making molecular vibrations audible in a range of experiences from rhythms, to harmony, to melodies. For sources of sonic content, we explore a variety of protein structures - virus spike protein alone, spike protein attached to human cell, human cell alone, and various states of the human cell alone. These provide the melodic foundation on which the progression is based. 

The track image is taken from [1], a recent study to make protein vibrations visible via water waves.

[1] M. Buehler, Liquified protein vibrations, classification and cross-paradigm de novo image generation using deep neural networks, https://arxiv.org/abs/2004.07603, 2020

Growth, Infection and Release

Markus J. Buehler is the McAfee Professor of Engineering at MIT, and a composer of experimental, classical and electronic music, with an interest in sonification. Using an approach termed "materiomusic", his artistic work explores the creation of new forms of musical expression - such as those derived from biological materials and living systems - as a means to better understand the underlying science and mathematics. One of his goals is to use musical and sound design as a novel and abstract way to model, optimize and create new forms of matter from the bottom up, and to assess cross-system design relationships. He is also interested in research to explore relationships between classical music, mathematics, and the physical and biological sciences, an in the mapping of models of consciousness across systems. In recent work he has developed a new framework to compose music based on proteins – the basic molecules of all life, as well as other physical phenomena such as fracturing, to explore similarities and differences across species, scales and between philosophical and physical models. 

Contact: mbuehler@MIT.EDU

Markus J. Buehler

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